I have transcriptomic datasets (control and treatment) with gene names and 5 cell lines as the columns.

What bioconductor pipelines can be used to detect gene signature in the treatment group compare with the control?

What in silico evidence can be used to determine the efficacy of the treatment when combined with a transcription factor inhibitor? Thanks.

This support site is meant to help people with technical questions about using Bioconductor packages. Your question is probably better suited to biostars.org.